Hi Sam.
If you still have any of your crystals or any protein solution left in the well
you harvested your crystals, I would run a MS/MS with them. Next step would be
to run AF with your known chain A and your best Mass Spec hit (s), and use the
resulting model for MR.
Good luck
Rafael Marques da Silva
PhD Student – Structural Biology
University of Leicester
Mestre em Física Biomolecular
Universidade de São Paulo
Bacharel em Ciências Biológicas
Universidade Federal de São Carlos
phone: +55 16 99766-0021
"A sorte acompanha uma mente bem treinada"
________________________________________________
________________________________
De: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> em nome de Boaz Shaanan
<bshaa...@bgu.ac.il>
Enviado: Monday, November 6, 2023 2:41:43 PM
Para: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
Assunto: Re: [ccp4bb] About model building
Hi,
If you still have crystals left, you could soak crystals with KI3 and collect
data at Cu wavelength for SAD phasing, which could help you to resolve the
missing piece. Maybe.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben Gurion University
Beer Sheva, Israel
On Nov 4, 2023 10:04, Sam Tang <samtys0...@gmail.com> wrote:
Dear community,
I am solving the structure of a complex between proteins A and B, where A is a
protein with known homologs and B is a novel protein isolated from plant. The
diffraction data was at 1.9 Ang collected in-house, indexed to P321. Using A as
the search model, we have got a reasonable solution where, after one round of
refinement, the A chain fits the map pretty well. What's left was to extend the
termini and fit a few rotamers.
For protein B (B chain) I have tried the web version of ARP/wARP but the
outcome was not really good. The model was not successfully built as indicated
by low model completeness and score. The tricky thing may be that we do not
have the complete sequence information of this protein B in-hand. (The other
way round, we more or less wish to rely on the high resolution data to confirm
its sequence.) What approach would you then recommend to build the B chain in
this scenario?
Thanks in advance and best regards,
Sam
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